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MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori

ABSTRACT: Background: The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production. Results: Here, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), including 728 novel miRNAs and 110 miRNA/miRNA* duplexes, from the posterior silk gland at the fifth larval instar. Target gene prediction yields 14,222 unique target genes from 1,195 miRNAs. Functional categorization classifies the genes into complex pathways that include both cellular and metabolic processes, especially protein synthesis and processing. Conclusion: The enrichment of target genes in the ribosome-related pathway indicates that miRNAs may directly regulate translation. Our findings pave a way for further functional elucidation of these miRNAs in silk production.

ORGANISM(S): Bombyx mori

PROVIDER: GSE56380 | GEO | 2014/07/30

SECONDARY ACCESSION(S): PRJNA243072

REPOSITORIES: GEO

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MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori

Project description:Background: The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production. Results: Here, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), including 728 novel miRNAs and 110 miRNA/miRNA* duplexes, from the posterior silk gland at the fifth larval instar. Target gene prediction yields 14,222 unique target genes from 1,195 miRNAs. Functional categorization classifies the genes into complex pathways that include both cellular and metabolic processes, especially protein synthesis and processing. Conclusion: The enrichment of target genes in the ribosome-related pathway indicates that miRNAs may directly regulate translation. Our findings pave a way for further functional elucidation of these miRNAs in silk production. Sequencing 10 total RNA samples from the posterior silk gland of different strains and developmental stage using Illumina Solexa technology. Four strains of silkworm (Q, B, QB and BQ) with different two development stages (stage 1: fourth instar molting to day 2 of fifth instar; stage 2: fifth instar day 3 to day 8 before spinning, according to our previous genes expression cluster analysis), and two strains (R1 and J1) from entire period (stage 1 + stage 2).

2014-07-30 | E-GEOD-56380 | biostudies-arrayexpress

Expression data from silkworm posterior silk glands at the late larval stages

2012-12-05 | GSE26172 | GEO

Proteome identification of the silkworm middle silk gland

Project description:The middle silk gland (MSG) is an important silkworm sub-organ for synthesis and secretion of sericin proteins. To investigate the proteome differences among the anterior, middle, and posterior regions of silkworm MSG at the third day of the fifth instar, the extracted tissue proteins were digested in gel with trypsin followed by shotgun LC-MS/MS analysis with a LTQ-Orbitrap mass spectrometer.

2016-03-11 | PXD003371 | Pride

Proteomic analysis of posterior silk gland of wild silkworm during developmental stages

Project description:We performed shotgun proteomic analysis of the posterior silk glands (PSGs) of wild silkworms on the 3rd and 5th days of the fifth instar.

2017-08-25 | PXD006655 | Pride

Expression data from silkworm posterior silk glands at the late larval stages

Project description:The silkworm silk gland is one of the most efficient protein synthesis systems among all organisms. Its amazingly efficient protein synthesis makes the silk gland a desirable object for basic studies on gene expression and regulation and for biotechnological applications. At the early stages of the fifth (final) instar, the cellular structures necessary for the synthesis of fibroin are rapidly formed, and at the later stage the synthesis of fibroin proceeds at a maximum rate. The posterior silk gland (PSG) is the longest suborgan and is responsible for the synthesis of the silk core protein fibroin, which is composed of heavy (H) and light (L) chains plus P25. We used microarrays to detail the global programme of gene expression in silkworm PSG during the late larval stages, including the fourth molting (M4) and day 1 (V1), day 3 (V3), day 5 (V5), and day 7 (wandering stage, W) of the fifth instar, and to reveal the correlations of differential expression genes with the PSG development and fibroin synthesis. Silkworm PSGs were collected at M4, V1, V3, V5, and W stages for RNA extraction and hybridization on 23K Silkworm Genome Arrays (CapitalBio Corp., Beijing, China). Three groups of biological replicates were prepared at each time point.Dual-dye experiments were performed for the PSG at M4, V1, V3, V5, and W; a total of 15 samples were tested including three biological replicates at each stage. Aliquots of each test sample were pooled as a common reference sample (CKA). The test samples and CKA were labeled with Cy3 and Cy5, respectively.

2012-12-05 | E-GEOD-26172 | biostudies-arrayexpress

The fourth instar in the silk gland of silkworm LC-MSMS

Project description:In the present study, the silk gland proteomes of the fourth instar and fourth molt were analyzed using liquid chromatography−tandem mass spectrometry. In total, 2654 proteins were identified from the silk gland. High abundance of ribosomal proteins and RR-motif chitin-binding proteins were identified during day 2 of the fourth instar (IV-2) larval developmental stage, and the expression of cuticular proteins analogous to peritrophin (CPAP)-motif chitin-binding proteins was higher during the fourth molt (IV-M). In all, nine enzymes were found to be involved in the chitin regeneration pathway in the silk gland. Among them, two chitinase and two chitin deacetylases were identified as CPAP-motif proteins.

2018-06-04 | PXD008677 | Pride

Bombyx mori Posterior and Median Silk Gland SAGE transcriptome

Project description:To identify functions that distinguish the posterior and median cells producing fibroin and sericin in the silk gland of Bombyx mori, serial analysis of gene expression (SAGE) profiles from both silk gland regions were analyzed and compared. The construction of a B. mori reference tag collection extracted from a set of 38000 Bombyx EST sequenced from the 3’ side, helped annotating the SAGE libraries. Most of the tags appeared at similar relative concentration in the two libraries except for those corresponding to silk proteins that were found region-specific and highly abundant. Strikingly, besides tags from silk protein mRNAs, 19 tags were found in the class of high abundance in the median cell library, which were absent in the posterior cell tag collection. Except tags from SP1 mRNA, no PSG specific tags were found in the same class of abundance. The analysis of MSG-specific different transcripts led to suggest that middle silk gland cell realizes more diversified functions as those already known, of synthesis and secretion of the silk sericins.

2010-12-22 | GSE23098 | GEO

The proteomics analyses of different tissues(the posterior silk gland of wild silkworm)

Project description:We collected a total of 9.8 million mass spectra data generated in the laboratory from the proteomics analyses of different silkworm tissues, including the posterior silk gland (29), middle silk gland (30), ovary and testis (31), head (32), brain, prothoracic glands, subesophageal ganglion (33), hemolymph (34), fat body (35) and embryo (36,37) of domestic silkworm, and the posterior silk gland of wild silkworm (38).

2019-07-01 | PXD009671 | Pride

Bombyx mori

Project description:MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori

| PRJNA243072 | ENA

Bombyx mori anterior silk gland LC-MS/MS

Project description:The anterior silk gland in the silkworm plays an important role in the process of liquid fibroin to solid silk fiber .In view of this,the proteomics analysis was applied to to study the relationship between the function of proteins in the anterior silk gland and the mechanism of spinning. The anterior silk glands on the 3rd day of fifth instar were dissected.Aftter 1D SDS-PAGE ,one gel lane was cut into 10 bands and each band further sliced into small pieces was subjected to in-gel tryptic digestion for 20 hours.The digested peptides were separated by RP nanoscale capillary liquid chromatography and analyzed using a surveyor LC system (Thermo Figgigan, San Jose, CA).The eluate from the RP column was analyzed by Finnigan LTQ(Thermo Electron Corporation）linear ion trap Mass equipped with a nanospray souce in the positive ion mode. The MS analysis was performed with one full MS scan followed by three MS/MS scans on the most intense ions from the MS spectrum with the dynamic exclusion settings: repeat count 2, repeat duration 30s, exclusion duration 90s. Data were acquired in data-dependent mode using Xcalibur software.Ten raw datasets from LC-MS/MS were searched against the predicted silkworm database by Xia.et al which consists of 21312 silkworm proteins.The searching was carried out with the Turbo SEQUEST(Bioworks version 3.2, Thermo Electron).

2014-03-26 | PXD000090 | Pride

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